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Answer: ROAST compare results with complex design
by
James W. MacDonald
68k
You are specifying that the last column of your design should be used as the contrast. You should instead use `contrast[,1]`, which will us…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
by
James W. MacDonald
68k
Yes. You can infer that by figuring out what each coefficient measures. Here is your design matrix:
```
> targets
ID Name phase G…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
by
snijesh
▴
200
I would like to clarify whether the command
`res <- results(dds, name = "phaseLP.conditionTreated")`
is the correct approach to generate …
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
by
James W. MacDonald
68k
Not sure I understand. You ask how to do something and then show how one would do so.
Comment: DiffBind getting Fold values of near 0
by
littlefishes20
▴
10
Same issues. All peaks return to a fold near 0, although they are significant when visualizing in IGV. Please find the MAplot and volcanoPl…
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